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The following doc has instructions for redirecting the agents to the new EM site:
Once you have the agent pointed to the new site, you can discover the database targets as you did previously.
The given link is saying that we need to remove the existing agent and need to deploy the agent again.
Only necessary to remove the Agent Home, a.k.a. Agent State Directory. The binary home should be kept.
Anyway, the instructions have been taken out of the book for review. Please hold off following them (if you have a copy of the old version of the manual).